Im pretty sure you can swap the heads with no problem so long as you use the corresponding head cover as its assumed they're machined to match. If you want to swap the engines altogether you should look at wiring diagrams first. I know you need a 95 or later CDI for 95 and later engines.

He's including the CDI box (even threw in the carb for $50).
Grabbing it from lilbill in the marketplace. He had good pictures and a video of it running, so I'm hoping everything is good to go, it started up pretty quickly. You thinking I need the wiring harness? Anybody know if the CDI box connectors are different, or just what's in them.

By the way BURN, there is a CDI box for a 95 on E-bay right now, I dropped the link on your request in the Marketplace

Good deal, glad you found one. Any idea what they control that is so model dependant?

Must be a sensor internal to the engine that tells it when to fire that is different. Any idea if it matters that everything else will be off an 87, coil, rectifier, wiring harness, etc? If all it is is the CDI box and a sensor internal to the engine I should be good. If not, I might as well just swap the head and leave it alone. I went through a lot of trouble to re-insulate/waterproof my entire electrical system and dress up and paint all the little electrical components and switches. Hate to start all that over again.

1st off the CDI's are not interchangable
not electronically nor physically

the timings different and the wiring different

so to use a 95 or later in a 88 or earlier wire loom,
you gotta change out the plugs

Yeah, I put a '96 engine in my '86.  I started it with the old CDI just to see what would happen.  It fired right up and idled fine but ran very badly.  The CDI connectors were different so I cut the connector off the '96 wiring harness and spliced it onto the '86.  Very simple, six wires with matching colors.  After that it ran fine.

Just like Verslagen1 said.